doubleFluxDel: Double Flux Deletion Experiment

In sybil: Efficient Constrained Based Modelling

Description

Double reaction (flux) deletion analysis.

Usage

  doubleFluxDel(model, react1, react2, lb = NULL, ub = NULL,
                allComb = FALSE, exex = FALSE, checkOptSolObj = FALSE, ...)

Arguments

model	An object of class modelorg.
react1	An object of class reactId or character or integer containing reaction id's to constrain to zero. Default: react_id(model).
react2	An object of class reactId or character or integer containing reaction id's to constrain to zero. Default: react_id(model).
lb	A numeric vector containing the lower bounds for the reaction rates of reactions (variables) given in arguments react1 and react2. If set to NULL, all reactions will be constrained to zero. Default: NULL.
ub	A numeric vector containing the upper bounds for the reaction rates of reactions (variables) given in arguments react1 and react2. If set to NULL, all reactions will be constrained to zero. Default: NULL.
allComb	A single Boolean value. If set to TRUE, every possible pairwise combination of reactions given in arguments react1 and react2 will be constrained to zero flux. If set to FALSE, arguments react1 and react2 must have the same length. The deletions will be computed pair-wise: first react1[1] and react2[1], second react1[2] and react2[2] and so on. Default: FALSE.
exex	A single Boolean value. If set to TRUE, exchange reactions will be excluded from the analysis. They are identified by the function findExchReact. Default: FALSE.
checkOptSolObj	A single logical value. If set to TRUE, a warning will be generated, if not all optimizations ended successful. Default: FALSE.
...	Further arguments passed to optimizer. Important ones are algorithm in order to set the algorithm to use or solverParm in order to set parameter values for the optimization software.

Details

The function doubleFluxDel studies the effect of double flux deletions on the phenotype of the metabolic network. The function performs n optimizations with n being either the number of reaction id's in argument react1 times the number of reaction id's in argument react2, if argument allComb is set to TRUE, or the length of one of these vectors if argument allComb is set to FALSE. Each optimization corresponds to the simultaneous deletion of two fluxes.

Value

An object of class optsol_fluxdel.

Author(s)

Gabriel Gelius-Dietrich <[e-mail]>

Maintainer: Mayo Roettger <[e-mail]>

See Also

modelorg, optsol, optsol_fluxdel, checkOptSol, optimizer and SYBIL_SETTINGS.

Examples

  data(Ec_core)
  Ec_dfd <- doubleFluxDel(Ec_core)

sybil documentation built on May 31, 2021, 5:08 p.m.